bamflagsplit

NAME

bamflagsplit - sort BAM files by coordinate or query name

DESCRIPTION

bamflagsplit reads a name collated BAM, SAM or CRAM file and distributes the contained reads into a set of BAM files. The reads are distributed as follows:

single: single end reads are placed in the single file

unmapped: (partially) unmapped read pairs (pairs where at least one of the two mates is unmapped) are placed in the unmapped file

orphan: orphan reads (pairs where the other mate is missing in the file) are placed in the orphan file

supplementary: supplementary mappings (mappings which have the supplementary flag set) are placed in the supplementary file

split: split pair reads (pairs such that the two ends map to different reference sequences/chromosomes) are placed in the split file

samestrand: read pairs such that both ends map to the same strand are placed in the samestrand file

improper: improperly mapped read pairs (read pairs where the mapped as a proper pair flag is not set) are place in the improper file

proper: properly mapped pairs are placed in the proper file

The following key=value pairs can be given:

I=<[stdin]>: input filename, standard input if unset.

level=<-1|0|1|9|11>: set compression level of the output BAM files. Valid values are

-1:: zlib/gzip default compression level

0:: uncompressed

1:: zlib/gzip level 1 (fast) compression

9:: zlib/gzip level 9 (best) compression

If libmaus has been compiled with support for igzip (see https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data) then an additional valid value is

11:: igzip compression

verbose=<1>: Valid values are

1:: print progress report on standard error

0:: do not print progress report

disablevalidation=<0|1>: sets whether input validation is performed. Valid values are

0:: validation is enabled (default)

1:: validation is disabled

single=<filename>: file name for the single file

singlemd5=<0|1>: md5 checksum creation for single output file. Valid values are

0:: do not compute checksum. This is the default.

1:: compute checksum. If the splitmd5filename key is set, then the checksum is written to the given file. If splitmd5filename, then no checksum will be computed.

unmapped=<filename>: file name for the unmapped file

unmappedmd5=<0|1>: md5 checksum creation for unmapped output file. Valid values are

0:: do not compute checksum. This is the default.

1:: compute checksum. If the splitmd5filename key is set, then the checksum is written to the given file. If splitmd5filename, then no checksum will be computed.

orphan=<filename>: file name for the orphan file

orphanmd5=<0|1>: md5 checksum creation for orphan output file. Valid values are

0:: do not compute checksum. This is the default.

1:: compute checksum. If the splitmd5filename key is set, then the checksum is written to the given file. If splitmd5filename, then no checksum will be computed.

supplementary=<filename>: file name for the supplementary file

supplementarymd5=<0|1>: md5 checksum creation for supplementary output file. Valid values are

0:: do not compute checksum. This is the default.

1:: compute checksum. If the splitmd5filename key is set, then the checksum is written to the given file. If splitmd5filename, then no checksum will be computed.

split=<filename>: file name for the split file

splitmd5=<0|1>: md5 checksum creation for split output file. Valid values are

0:: do not compute checksum. This is the default.

1:: compute checksum. If the splitmd5filename key is set, then the checksum is written to the given file. If splitmd5filename, then no checksum will be computed.

samestrand=<filename>: file name for the samestrand file

samestrandmd5=<0|1>: md5 checksum creation for samestrand output file. Valid values are

0:: do not compute checksum. This is the default.

1:: compute checksum. If the samestrandmd5filename key is set, then the checksum is written to the given file. If samestrandmd5filename, then no checksum will be computed.

improper=<filename>: file name for the improper file

impropermd5=<0|1>: md5 checksum creation for improper output file. Valid values are

0:: do not compute checksum. This is the default.

1:: compute checksum. If the impropermd5filename key is set, then the checksum is written to the given file. If impropermd5filename, then no checksum will be computed.

proper=<filename>: file name for the proper file

propermd5=<0|1>: md5 checksum creation for proper output file. Valid values are

0:: do not compute checksum. This is the default.

1:: compute checksum. If the propermd5filename key is set, then the checksum is written to the given file. If propermd5filename, then no checksum will be computed.

inputformat=<bam>: input file format. All versions of bamflagsplit come with support for the BAM input format. If the program in addition is linked to the io_lib package, then the following options are valid: